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Conserved domains on  [gi|22024390|ref|NP_647479|]
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potassium voltage-gated channel subfamily H member 5 isoform 1 [Homo sapiens]

Protein Classification

PAS and CAP_ED domain-containing protein( domain architecture ID 13822715)

protein containing domains PAS, CAP_ED, and Crp

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03192 super family cl33658
Voltage-dependent potassium channel; Provisional
 217-616 4.46e-35

Voltage-dependent potassium channel; Provisional


The actual alignment was detected with superfamily member PLN03192:

Pssm-ID: 215625 [Multi-domain]  Cd Length: 823  Bit Score: 144.24  E-value: 4.46e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390  217 WDWVILILTFYTAIMVPYNVSFKTKQNNIAWLVLDSVVDVIFLVDIVLNFHTTFVGPGGEV-ISDPKLIRMNYLKTWFVI 295
Cdd:PLN03192  64 WETLMVVLVAYSAWVYPFEVAFLNASPKRGLEIADNVVDLFFAVDIVLTFFVAYIDPRTQLlVRDRKKIAVRYLSTWFLM 143

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390  296 DLLSCLPYDIINAFENVDEGISSLFSSLKVVRLLRLGRVAR-----KLDHYLEYGAAVLVLLVCVFGLVAHWLACIWYSI 370
Cdd:PLN03192 144 DVASTIPFQALAYLITGTVKLNLSYSLLGLLRFWRLRRVKQlftrlEKDIRFSYFWIRCARLLSVTLFLVHCAGCLYYLI 223

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390  371 GDyevidevtntiqidswlyqlalsigtpyRYNTSAGIWEGG--PS--KDSL---YVSSLYFTMTSLTTIGFGNIAPTTD 443
Cdd:PLN03192 224 AD----------------------------RYPHQGKTWIGAviPNfrETSLwirYISAIYWSITTMTTVGYGDLHAVNT 275

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390  444 VEKMFSVAMMMVGSLLYATIFGNVTTIFQQmyaNTNRYHEMLNNVR---DFLKLYQVPKGLSERVMDYIVSTWSmSKGID 520
Cdd:PLN03192 276 IEMIFIIFYMLFNLGLTAYLIGNMTNLVVE---GTRRTMEFRNSIEaasNFVGRNRLPPRLKDQILAYMCLRFK-AESLN 351

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390  521 TEKVLSICPKDMRADICVHLNRKVFNEHPAFRLASDGCLRALAVEFQTIHCAPGDLIYHAGESVDALCFVVSGSLEVI-- 598
Cdd:PLN03192 352 QQQLIDQLPKSICKSICQHLFLPVVEKVYLFKGVSREILLLLVTKMKAEYIPPREDVIMQNEAPDDVYIVVSGEVEIIds 431

                        410       420
                 ....*....|....*....|
gi 22024390  599 --QDDEVVAILGKGDVFGDI 616
Cdd:PLN03192 432 egEKERVVGTLGCGDIFGEV 451
PAS_9 pfam13426
PAS domain; This domain is found in many signalling proteins in which it functions as a sensor ...
 39-132 2.08e-16

PAS domain; This domain is found in many signalling proteins in which it functions as a sensor domain. It recognizes FMN, Zn(II), FAD and riboflavin (MAtilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


:

Pssm-ID: 463873 [Multi-domain]  Cd Length: 93  Bit Score: 75.19  E-value: 2.08e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390    39 PVVYSNDGFCKLSGYHRADVMQKSstCSFMYGELTDKKTIEKVRQTFDnyESNCFEVLLYKKNRTPVWFYMQIAPIRNEH 118
Cdd:pfam13426   3 RIIYVNDAALRLLGYTREELLGKS--ITDLFAEPEDSERLREALREGK--AVREFEVVLYRKDGEPFPVLVSLAPIRDDG 78

                          90
                  ....*....|....
gi 22024390   119 EKVVLFLCTFKDIT 132
Cdd:pfam13426  79 GELVGIIAILRDIT 92
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 551-758 1.17e-14

cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms];


:

Pssm-ID: 440428 [Multi-domain]  Cd Length: 207  Bit Score: 73.87  E-value: 1.17e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390 551 FRLASDGCLRALAVEFQTIHCAPGDLIYHAGESVDALCFVVSGSLEVIQDDE-----VVAILGKGDVFGDIFWkeTTLAH 625
Cdd:COG0664   1 FAGLSDEELEALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRISEdgreqILGFLGPGDFFGELSL--LGGEP 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390 626 ACANVRALTYCDLHIIKREALLKVLDFYTAFANSFSRNLT-LTCNLRKRIIFRKISDVkkeeEERL---------RQKNE 695
Cdd:COG0664  79 SPATAEALEDSELLRIPREDLEELLERNPELARALLRLLArRLRQLQERLVSLAFLSA----EERLarflleladRLDGR 154

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 22024390 696 VTLSIPvdhpvrklfqkfkqQKELrnqgstqgdpernqlqvesrslqngASITGTSVVTVSQI 758
Cdd:COG0664 155 IDLPLT--------------QEEI-------------------------ASYLGLTRETVSRI 178
 
Name Accession Description Interval E-value
PLN03192 PLN03192
Voltage-dependent potassium channel; Provisional
 217-616 4.46e-35

Voltage-dependent potassium channel; Provisional


Pssm-ID: 215625 [Multi-domain]  Cd Length: 823  Bit Score: 144.24  E-value: 4.46e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390  217 WDWVILILTFYTAIMVPYNVSFKTKQNNIAWLVLDSVVDVIFLVDIVLNFHTTFVGPGGEV-ISDPKLIRMNYLKTWFVI 295
Cdd:PLN03192  64 WETLMVVLVAYSAWVYPFEVAFLNASPKRGLEIADNVVDLFFAVDIVLTFFVAYIDPRTQLlVRDRKKIAVRYLSTWFLM 143

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390  296 DLLSCLPYDIINAFENVDEGISSLFSSLKVVRLLRLGRVAR-----KLDHYLEYGAAVLVLLVCVFGLVAHWLACIWYSI 370
Cdd:PLN03192 144 DVASTIPFQALAYLITGTVKLNLSYSLLGLLRFWRLRRVKQlftrlEKDIRFSYFWIRCARLLSVTLFLVHCAGCLYYLI 223

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390  371 GDyevidevtntiqidswlyqlalsigtpyRYNTSAGIWEGG--PS--KDSL---YVSSLYFTMTSLTTIGFGNIAPTTD 443
Cdd:PLN03192 224 AD----------------------------RYPHQGKTWIGAviPNfrETSLwirYISAIYWSITTMTTVGYGDLHAVNT 275

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390  444 VEKMFSVAMMMVGSLLYATIFGNVTTIFQQmyaNTNRYHEMLNNVR---DFLKLYQVPKGLSERVMDYIVSTWSmSKGID 520
Cdd:PLN03192 276 IEMIFIIFYMLFNLGLTAYLIGNMTNLVVE---GTRRTMEFRNSIEaasNFVGRNRLPPRLKDQILAYMCLRFK-AESLN 351

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390  521 TEKVLSICPKDMRADICVHLNRKVFNEHPAFRLASDGCLRALAVEFQTIHCAPGDLIYHAGESVDALCFVVSGSLEVI-- 598
Cdd:PLN03192 352 QQQLIDQLPKSICKSICQHLFLPVVEKVYLFKGVSREILLLLVTKMKAEYIPPREDVIMQNEAPDDVYIVVSGEVEIIds 431

                        410       420
                 ....*....|....*....|
gi 22024390  599 --QDDEVVAILGKGDVFGDI 616
Cdd:PLN03192 432 egEKERVVGTLGCGDIFGEV 451
Ion_trans pfam00520
Ion transport protein; This family contains sodium, potassium and calcium ion channels. This ...
 217-479 1.58e-34

Ion transport protein; This family contains sodium, potassium and calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane.


Pssm-ID: 459842 [Multi-domain]  Cd Length: 238  Bit Score: 132.39  E-value: 1.58e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390   217 WDWVILILTFYTAIMVPYNVSFKTKQ-NNIAWLVLDSVVDVIFLVDIVLNFHTTFvgpggevisdpklIRMNYLKT-WFV 294
Cdd:pfam00520   4 FELFILLLILLNTIFLALETYFQPEEpLTTVLEILDYVFTGIFTLEMLLKIIAAG-------------FKKRYFRSpWNI 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390   295 IDLLSCLPYDIInaFENVDEGISSLFSSLKVVRLLRLGRVARKLDHYLEYGAAVL--VLLVCVFGLVAHWLACIWYSIGd 372
Cdd:pfam00520  71 LDFVVVLPSLIS--LVLSSVGSLSGLRVLRLLRLLRLLRLIRRLEGLRTLVNSLIrsLKSLGNLLLLLLLFLFIFAIIG- 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390   373 yevidevtntiqidswlYQLalsigtpyrYNTSAGIWEGGPSKDSL---YVSSLYFTMTSLTTIGFGNIAPTTDVEK--- 446
Cdd:pfam00520 148 -----------------YQL---------FGGKLKTWENPDNGRTNfdnFPNAFLWLFQTMTTEGWGDIMYDTIDGKgef 201

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 22024390   447 ----MFSVAMMMVGSLLYATIFGNVTTIFQQMYANTN 479
Cdd:pfam00520 202 wayiYFVSFIILGGFLLLNLFIAVIIDNFQELTERTE 238
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 550-660 1.15e-22

effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels


Pssm-ID: 237999 [Multi-domain]  Cd Length: 115  Bit Score: 93.93  E-value: 1.15e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390 550 AFRLASDGCLRALAVEFQTIHCAPGDLIYHAGESVDALCFVVSGSLEVIQDDE-----VVAILGKGDVFGDIFWkeTTLA 624
Cdd:cd00038   1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEdgreqIVGFLGPGDLFGELAL--LGNG 78

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 22024390 625 HACANVRALTYCDLHIIKREALLKVLDFYTAFANSF 660
Cdd:cd00038  79 PRSATVRALTDSELLVLPRSDFRRLLQEYPELARRL 114
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 551-650 1.63e-16

Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.


Pssm-ID: 197516 [Multi-domain]  Cd Length: 120  Bit Score: 76.67  E-value: 1.63e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390    551 FRLASDGCLRALAVEFQTIHCAPGDLIYHAGESVDALCFVVSGSLEVIQDDE-----VVAILGKGDVFGDIFWKETTLAH 625
Cdd:smart00100   2 FKNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLEdgeeqIVGTLGPGDFFGELALLTNSRRA 81

                           90       100
                   ....*....|....*....|....*
gi 22024390    626 ACANVRALTYCDLHIIKREALLKVL 650
Cdd:smart00100  82 ASAAAVALELATLLRIDFRDFLQLL 106
PAS_9 pfam13426
PAS domain; This domain is found in many signalling proteins in which it functions as a sensor ...
 39-132 2.08e-16

PAS domain; This domain is found in many signalling proteins in which it functions as a sensor domain. It recognizes FMN, Zn(II), FAD and riboflavin (MAtilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 463873 [Multi-domain]  Cd Length: 93  Bit Score: 75.19  E-value: 2.08e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390    39 PVVYSNDGFCKLSGYHRADVMQKSstCSFMYGELTDKKTIEKVRQTFDnyESNCFEVLLYKKNRTPVWFYMQIAPIRNEH 118
Cdd:pfam13426   3 RIIYVNDAALRLLGYTREELLGKS--ITDLFAEPEDSERLREALREGK--AVREFEVVLYRKDGEPFPVLVSLAPIRDDG 78

                          90
                  ....*....|....
gi 22024390   119 EKVVLFLCTFKDIT 132
Cdd:pfam13426  79 GELVGIIAILRDIT 92
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 551-758 1.17e-14

cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms];


Pssm-ID: 440428 [Multi-domain]  Cd Length: 207  Bit Score: 73.87  E-value: 1.17e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390 551 FRLASDGCLRALAVEFQTIHCAPGDLIYHAGESVDALCFVVSGSLEVIQDDE-----VVAILGKGDVFGDIFWkeTTLAH 625
Cdd:COG0664   1 FAGLSDEELEALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRISEdgreqILGFLGPGDFFGELSL--LGGEP 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390 626 ACANVRALTYCDLHIIKREALLKVLDFYTAFANSFSRNLT-LTCNLRKRIIFRKISDVkkeeEERL---------RQKNE 695
Cdd:COG0664  79 SPATAEALEDSELLRIPREDLEELLERNPELARALLRLLArRLRQLQERLVSLAFLSA----EERLarflleladRLDGR 154

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 22024390 696 VTLSIPvdhpvrklfqkfkqQKELrnqgstqgdpernqlqvesrslqngASITGTSVVTVSQI 758
Cdd:COG0664 155 IDLPLT--------------QEEI-------------------------ASYLGLTRETVSRI 178
PAS COG2202
PAS domain [Signal transduction mechanisms];
37-136 1.51e-13

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 71.59  E-value: 1.51e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390  37 DWPVVYSNDGFCKLSGYHRADVMQKssTCSFMYGELTDKKTIEKVRQTFDNYESNCFEVLLYKKNRTPVWFYMQIAPIRN 116
Cdd:COG2202  30 DGRILYVNPAFERLTGYSAEELLGK--TLRDLLPPEDDDEFLELLRAALAGGGVWRGELRNRRKDGSLFWVELSISPVRD 107

                        90       100
                ....*....|....*....|
gi 22024390 117 EHEKVVLFLCTFKDITLFKQ 136
Cdd:COG2202 108 EDGEITGFVGIARDITERKR 127
PRK13558 PRK13558
bacterio-opsin activator; Provisional
 37-132 1.08e-10

bacterio-opsin activator; Provisional


Pssm-ID: 237426 [Multi-domain]  Cd Length: 665  Bit Score: 65.63  E-value: 1.08e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390   37 DWPVVYSNDGFCKLSGYHRADVMQKSstCSFMYGELTDKKTIEKVRQTFDNYESNCFEVLLYKKNRTPVWFYMQIAPIRN 116
Cdd:PRK13558 170 DEPLIYINDAFERITGYSPDEVLGRN--CRFLQGEDTNEERVAELREAIDEERPTSVELRNYRKDGSTFWNQVDIAPIRD 247

                         90
                 ....*....|....*.
gi 22024390  117 EHEKVVLFLCTFKDIT 132
Cdd:PRK13558 248 EDGTVTHYVGFQTDVT 263
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 37-131 5.09e-08

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 51.87  E-value: 5.09e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390  37 DWPVVYSNDGFCKLSGYHRADVMQKSSTcSFMYGEltDKKTI-EKVRQTFDNYESNCFEVLLYKKNRTPVWFYMQIAPIR 115
Cdd:cd00130  11 DGRILYANPAAEQLLGYSPEELIGKSLL-DLIHPE--DREELrERLENLLSGGEPVTLEVRLRRKDGSVIWVLVSLTPIR 87

                        90
                ....*....|....*.
gi 22024390 116 NEHEKVVLFLCTFKDI 131
Cdd:cd00130  88 DEGGEVIGLLGVVRDI 103
PAC smart00086
Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif ...
 93-132 4.67e-06

Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold.


Pssm-ID: 197509  Cd Length: 43  Bit Score: 44.10  E-value: 4.67e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 22024390     93 FEVLLYKKNRTPVWFYMQIAPIRNEHEKVVLFLCTFKDIT 132
Cdd:smart00086   2 VEYRLRRKDGSYIWVLVSASPIRDEDGEVEGILGVVRDIT 41
cyc_nuc_ocin TIGR03896
bacteriocin-type transport-associated protein; Members of this protein family are ...
 574-673 2.03e-03

bacteriocin-type transport-associated protein; Members of this protein family are uncharacterized and contain two copies of the cyclic nucleotide-binding domain pfam00027. Members are restricted to select cyanobacteria but are found regularly in association with a transport operon that, in turn, is associated with the production of putative bacteriocins. The models describing the transport operon are TIGR03794, TIGR03796, and TIGR03797.


Pssm-ID: 274839 [Multi-domain]  Cd Length: 317  Bit Score: 41.42  E-value: 2.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390   574 GDLIYHAGESVDALCFVVSGSLEV-IQDDE---VVAILGKGDVFGDIFWKETTLAhACANVRALTYCDLHIIKREALLKV 649
Cdd:TIGR03896 169 GTILIHEGGTVDALYILLYGEASLsISPDGpgrEVGSSRRGEILGETPFLNGSLP-GTATVKAIENSVLLAIDKQQLAAK 247

                          90       100
                  ....*....|....*....|....
gi 22024390   650 LDFYTAFANSFSRNLTLTCNLRKR 673
Cdd:TIGR03896 248 LQQDVGFASRFYRVIASLLSQRSR 271
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 14-132 3.31e-03

PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. [Regulatory functions, Small molecule interactions]


Pssm-ID: 272971 [Multi-domain]  Cd Length: 124  Bit Score: 38.43  E-value: 3.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390    14 TFLENIVRRSSESSFLLG-NAQIVDWpvvysNDGFCKLSGYHRADVMQKSSTcSFMYGELTDK--KTIEKVRQTFDNYES 90
Cdd:TIGR00229   3 ERYRAIFESSPDAIIVIDlEGNILYV-----NPAFEEIFGYSAEELIGRNVL-ELIPEEDREEvrERIERRLEGEPEPVS 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 22024390    91 NCFEVllYKKNRTPVWFYMQIAPIRnEHEKVVLFLCTFKDIT 132
Cdd:TIGR00229  77 EERRV--RRKDGSEIWVEVSVSPIR-TNGGELGVVGIVRDIT 115
 
Name Accession Description Interval E-value
PLN03192 PLN03192
Voltage-dependent potassium channel; Provisional
 217-616 4.46e-35

Voltage-dependent potassium channel; Provisional


Pssm-ID: 215625 [Multi-domain]  Cd Length: 823  Bit Score: 144.24  E-value: 4.46e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390  217 WDWVILILTFYTAIMVPYNVSFKTKQNNIAWLVLDSVVDVIFLVDIVLNFHTTFVGPGGEV-ISDPKLIRMNYLKTWFVI 295
Cdd:PLN03192  64 WETLMVVLVAYSAWVYPFEVAFLNASPKRGLEIADNVVDLFFAVDIVLTFFVAYIDPRTQLlVRDRKKIAVRYLSTWFLM 143

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390  296 DLLSCLPYDIINAFENVDEGISSLFSSLKVVRLLRLGRVAR-----KLDHYLEYGAAVLVLLVCVFGLVAHWLACIWYSI 370
Cdd:PLN03192 144 DVASTIPFQALAYLITGTVKLNLSYSLLGLLRFWRLRRVKQlftrlEKDIRFSYFWIRCARLLSVTLFLVHCAGCLYYLI 223

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390  371 GDyevidevtntiqidswlyqlalsigtpyRYNTSAGIWEGG--PS--KDSL---YVSSLYFTMTSLTTIGFGNIAPTTD 443
Cdd:PLN03192 224 AD----------------------------RYPHQGKTWIGAviPNfrETSLwirYISAIYWSITTMTTVGYGDLHAVNT 275

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390  444 VEKMFSVAMMMVGSLLYATIFGNVTTIFQQmyaNTNRYHEMLNNVR---DFLKLYQVPKGLSERVMDYIVSTWSmSKGID 520
Cdd:PLN03192 276 IEMIFIIFYMLFNLGLTAYLIGNMTNLVVE---GTRRTMEFRNSIEaasNFVGRNRLPPRLKDQILAYMCLRFK-AESLN 351

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390  521 TEKVLSICPKDMRADICVHLNRKVFNEHPAFRLASDGCLRALAVEFQTIHCAPGDLIYHAGESVDALCFVVSGSLEVI-- 598
Cdd:PLN03192 352 QQQLIDQLPKSICKSICQHLFLPVVEKVYLFKGVSREILLLLVTKMKAEYIPPREDVIMQNEAPDDVYIVVSGEVEIIds 431

                        410       420
                 ....*....|....*....|
gi 22024390  599 --QDDEVVAILGKGDVFGDI 616
Cdd:PLN03192 432 egEKERVVGTLGCGDIFGEV 451
Ion_trans pfam00520
Ion transport protein; This family contains sodium, potassium and calcium ion channels. This ...
 217-479 1.58e-34

Ion transport protein; This family contains sodium, potassium and calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane.


Pssm-ID: 459842 [Multi-domain]  Cd Length: 238  Bit Score: 132.39  E-value: 1.58e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390   217 WDWVILILTFYTAIMVPYNVSFKTKQ-NNIAWLVLDSVVDVIFLVDIVLNFHTTFvgpggevisdpklIRMNYLKT-WFV 294
Cdd:pfam00520   4 FELFILLLILLNTIFLALETYFQPEEpLTTVLEILDYVFTGIFTLEMLLKIIAAG-------------FKKRYFRSpWNI 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390   295 IDLLSCLPYDIInaFENVDEGISSLFSSLKVVRLLRLGRVARKLDHYLEYGAAVL--VLLVCVFGLVAHWLACIWYSIGd 372
Cdd:pfam00520  71 LDFVVVLPSLIS--LVLSSVGSLSGLRVLRLLRLLRLLRLIRRLEGLRTLVNSLIrsLKSLGNLLLLLLLFLFIFAIIG- 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390   373 yevidevtntiqidswlYQLalsigtpyrYNTSAGIWEGGPSKDSL---YVSSLYFTMTSLTTIGFGNIAPTTDVEK--- 446
Cdd:pfam00520 148 -----------------YQL---------FGGKLKTWENPDNGRTNfdnFPNAFLWLFQTMTTEGWGDIMYDTIDGKgef 201

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 22024390   447 ----MFSVAMMMVGSLLYATIFGNVTTIFQQMYANTN 479
Cdd:pfam00520 202 wayiYFVSFIILGGFLLLNLFIAVIIDNFQELTERTE 238
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 550-660 1.15e-22

effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels


Pssm-ID: 237999 [Multi-domain]  Cd Length: 115  Bit Score: 93.93  E-value: 1.15e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390 550 AFRLASDGCLRALAVEFQTIHCAPGDLIYHAGESVDALCFVVSGSLEVIQDDE-----VVAILGKGDVFGDIFWkeTTLA 624
Cdd:cd00038   1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEdgreqIVGFLGPGDLFGELAL--LGNG 78

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 22024390 625 HACANVRALTYCDLHIIKREALLKVLDFYTAFANSF 660
Cdd:cd00038  79 PRSATVRALTDSELLVLPRSDFRRLLQEYPELARRL 114
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 551-650 1.63e-16

Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.


Pssm-ID: 197516 [Multi-domain]  Cd Length: 120  Bit Score: 76.67  E-value: 1.63e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390    551 FRLASDGCLRALAVEFQTIHCAPGDLIYHAGESVDALCFVVSGSLEVIQDDE-----VVAILGKGDVFGDIFWKETTLAH 625
Cdd:smart00100   2 FKNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLEdgeeqIVGTLGPGDFFGELALLTNSRRA 81

                           90       100
                   ....*....|....*....|....*
gi 22024390    626 ACANVRALTYCDLHIIKREALLKVL 650
Cdd:smart00100  82 ASAAAVALELATLLRIDFRDFLQLL 106
PAS_9 pfam13426
PAS domain; This domain is found in many signalling proteins in which it functions as a sensor ...
 39-132 2.08e-16

PAS domain; This domain is found in many signalling proteins in which it functions as a sensor domain. It recognizes FMN, Zn(II), FAD and riboflavin (MAtilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 463873 [Multi-domain]  Cd Length: 93  Bit Score: 75.19  E-value: 2.08e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390    39 PVVYSNDGFCKLSGYHRADVMQKSstCSFMYGELTDKKTIEKVRQTFDnyESNCFEVLLYKKNRTPVWFYMQIAPIRNEH 118
Cdd:pfam13426   3 RIIYVNDAALRLLGYTREELLGKS--ITDLFAEPEDSERLREALREGK--AVREFEVVLYRKDGEPFPVLVSLAPIRDDG 78

                          90
                  ....*....|....
gi 22024390   119 EKVVLFLCTFKDIT 132
Cdd:pfam13426  79 GELVGIIAILRDIT 92
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 551-758 1.17e-14

cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms];


Pssm-ID: 440428 [Multi-domain]  Cd Length: 207  Bit Score: 73.87  E-value: 1.17e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390 551 FRLASDGCLRALAVEFQTIHCAPGDLIYHAGESVDALCFVVSGSLEVIQDDE-----VVAILGKGDVFGDIFWkeTTLAH 625
Cdd:COG0664   1 FAGLSDEELEALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRISEdgreqILGFLGPGDFFGELSL--LGGEP 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390 626 ACANVRALTYCDLHIIKREALLKVLDFYTAFANSFSRNLT-LTCNLRKRIIFRKISDVkkeeEERL---------RQKNE 695
Cdd:COG0664  79 SPATAEALEDSELLRIPREDLEELLERNPELARALLRLLArRLRQLQERLVSLAFLSA----EERLarflleladRLDGR 154

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 22024390 696 VTLSIPvdhpvrklfqkfkqQKELrnqgstqgdpernqlqvesrslqngASITGTSVVTVSQI 758
Cdd:COG0664 155 IDLPLT--------------QEEI-------------------------ASYLGLTRETVSRI 178
PAS COG2202
PAS domain [Signal transduction mechanisms];
37-136 1.51e-13

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 71.59  E-value: 1.51e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390  37 DWPVVYSNDGFCKLSGYHRADVMQKssTCSFMYGELTDKKTIEKVRQTFDNYESNCFEVLLYKKNRTPVWFYMQIAPIRN 116
Cdd:COG2202  30 DGRILYVNPAFERLTGYSAEELLGK--TLRDLLPPEDDDEFLELLRAALAGGGVWRGELRNRRKDGSLFWVELSISPVRD 107

                        90       100
                ....*....|....*....|
gi 22024390 117 EHEKVVLFLCTFKDITLFKQ 136
Cdd:COG2202 108 EDGEITGFVGIARDITERKR 127
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 569-651 1.57e-12

Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, oxygen and 2-oxoglutarate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 459637 [Multi-domain]  Cd Length: 89  Bit Score: 64.17  E-value: 1.57e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390   569 IHCAPGDLIYHAGESVDALCFVVSGSLEVIQDDE-----VVAILGKGDVFGD--IFwketTLAHACANVRALTYCDLHII 641
Cdd:pfam00027   2 RSYKAGEVIFREGDPADSLYIVLSGKVKVYRTLEdgreqILAVLGPGDFFGElaLL----GGEPRSATVVALTDSELLVI 77

                          90
                  ....*....|
gi 22024390   642 KREALLKVLD 651
Cdd:pfam00027  78 PREDFLELLE 87
Ion_trans_2 pfam07885
Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
 419-473 3.26e-12

Ion channel; This family includes the two membrane helix type ion channels found in bacteria.


Pssm-ID: 462301 [Multi-domain]  Cd Length: 78  Bit Score: 62.67  E-value: 3.26e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 22024390   419 YVSSLYFTMTSLTTIGFGNIAPTTDVEKMFSVAMMMVGSLLYATIFGNVTTIFQQ 473
Cdd:pfam07885  24 FLDALYFSFVTLTTVGYGDIVPLTDAGRLFTIFYILIGIPLFAIFLAVLGRFLTE 78
PRK13558 PRK13558
bacterio-opsin activator; Provisional
 37-132 1.08e-10

bacterio-opsin activator; Provisional


Pssm-ID: 237426 [Multi-domain]  Cd Length: 665  Bit Score: 65.63  E-value: 1.08e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390   37 DWPVVYSNDGFCKLSGYHRADVMQKSstCSFMYGELTDKKTIEKVRQTFDNYESNCFEVLLYKKNRTPVWFYMQIAPIRN 116
Cdd:PRK13558 170 DEPLIYINDAFERITGYSPDEVLGRN--CRFLQGEDTNEERVAELREAIDEERPTSVELRNYRKDGSTFWNQVDIAPIRD 247

                         90
                 ....*....|....*.
gi 22024390  117 EHEKVVLFLCTFKDIT 132
Cdd:PRK13558 248 EDGTVTHYVGFQTDVT 263
PRK13557 PRK13557
histidine kinase; Provisional
 37-132 1.55e-08

histidine kinase; Provisional


Pssm-ID: 237425 [Multi-domain]  Cd Length: 540  Bit Score: 58.53  E-value: 1.55e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390   37 DWPVVYSNDGFCKLSGYHRADVMqkSSTCSFMYGELTDKKTIEKVRQTFDNYESNCFEVLLYKKNRTPVWFYMQIAPIRN 116
Cdd:PRK13557  52 DNPIVFANRAFLEMTGYAAEEII--GNNCRFLQGPETDRATVAEVRDAIAERREIATEILNYRKDGSSFWNALFVSPVYN 129

                         90
                 ....*....|....*.
gi 22024390  117 EHEKVVLFLCTFKDIT 132
Cdd:PRK13557 130 DAGDLVYFFGSQLDVS 145
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 37-131 5.09e-08

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 51.87  E-value: 5.09e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390  37 DWPVVYSNDGFCKLSGYHRADVMQKSSTcSFMYGEltDKKTI-EKVRQTFDNYESNCFEVLLYKKNRTPVWFYMQIAPIR 115
Cdd:cd00130  11 DGRILYANPAAEQLLGYSPEELIGKSLL-DLIHPE--DREELrERLENLLSGGEPVTLEVRLRRKDGSVIWVLVSLTPIR 87

                        90
                ....*....|....*.
gi 22024390 116 NEHEKVVLFLCTFKDI 131
Cdd:cd00130  88 DEGGEVIGLLGVVRDI 103
PRK13559 PRK13559
hypothetical protein; Provisional
 37-132 6.07e-08

hypothetical protein; Provisional


Pssm-ID: 237427 [Multi-domain]  Cd Length: 361  Bit Score: 55.98  E-value: 6.07e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390   37 DWPVVYSNDGFCKLSGYHRADVMQKSstCSFMYGELTDKKTIEKVRQTFDNYESNCFEVLLYKKNRTPVWFYMQIAPIRN 116
Cdd:PRK13559  65 DLPIVLANQAFLDLTGYAAEEVVGRN--CRFLQGAATDPIAVAKIRAAIAAEREIVVELLNYRKDGEPFWNALHLGPVYG 142

                         90
                 ....*....|....*.
gi 22024390  117 EHEKVVLFLCTFKDIT 132
Cdd:PRK13559 143 EDGRLLYFFGSQWDVT 158
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 40-131 2.54e-06

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 395786 [Multi-domain]  Cd Length: 113  Bit Score: 47.41  E-value: 2.54e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390    40 VVYSNDGFCKLSGYHRADVMQKS-STCSFMYGELTDKKTIEKVRQTFDnyESNCFEVLLYKKNRTPVWFYMQIAPIRNEH 118
Cdd:pfam00989  23 ILYVNAAAEELLGLSREEVIGKSlLDLIPEEDDAEVAELLRQALLQGE--ESRGFEVSFRVPDGRPRHVEVRASPVRDAG 100

                          90
                  ....*....|...
gi 22024390   119 EKVVLFLCTFKDI 131
Cdd:pfam00989 101 GEILGFLGVLRDI 113
PAC smart00086
Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif ...
 93-132 4.67e-06

Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold.


Pssm-ID: 197509  Cd Length: 43  Bit Score: 44.10  E-value: 4.67e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 22024390     93 FEVLLYKKNRTPVWFYMQIAPIRNEHEKVVLFLCTFKDIT 132
Cdd:smart00086   2 VEYRLRRKDGSYIWVLVSASPIRDEDGEVEGILGVVRDIT 41
PRK11753 PRK11753
cAMP-activated global transcriptional regulator CRP;
577-638 3.73e-05

cAMP-activated global transcriptional regulator CRP;


Pssm-ID: 236969 [Multi-domain]  Cd Length: 211  Bit Score: 45.74  E-value: 3.73e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 22024390  577 IYHAGESVDALCFVVSGSLEVIQDDE-----VVAILGKGDVFGDIFWKETTLAHAcANVRALTYCDL 638
Cdd:PRK11753  31 LIHAGEKAETLYYIVKGSVAVLIKDEegkemILSYLNQGDFIGELGLFEEGQERS-AWVRAKTACEV 96
PRK10537 PRK10537
voltage-gated potassium channel protein;
420-467 1.68e-04

voltage-gated potassium channel protein;


Pssm-ID: 236711 [Multi-domain]  Cd Length: 393  Bit Score: 45.01  E-value: 1.68e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 22024390  420 VSSLYFTMTSLTTIGFGNIAPTTDVEKMFSVAMMMVGSLLYAT----IFGNV 467
Cdd:PRK10537 170 STAFYFSIVTMSTVGYGDIVPVSESARLFTISVIILGITVFATsisaIFGPV 221
NtrB COG3852
Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];
40-136 5.61e-04

Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];


Pssm-ID: 443061 [Multi-domain]  Cd Length: 361  Bit Score: 43.30  E-value: 5.61e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390  40 VVYSNDGFCKLSGYHRADVMQKSSTCSFMYGELtDKKTIEKVRQTfdNYESNCFEVLLYKKNRTPVWFYMQIAPIRNEHE 119
Cdd:COG3852  29 ITYVNPAAERLLGLSAEELLGRPLAELFPEDSP-LRELLERALAE--GQPVTEREVTLRRKDGEERPVDVSVSPLRDAEG 105

                        90
                ....*....|....*..
gi 22024390 120 KvVLFLCTFKDITLFKQ 136
Cdd:COG3852 106 E-GGVLLVLRDITERKR 121
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 40-127 1.39e-03

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.


Pssm-ID: 430001 [Multi-domain]  Cd Length: 89  Bit Score: 38.86  E-value: 1.39e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390    40 VVYSNDGFCKLSGYHRADVMQKSSTC-SFMYGEltDkktIEKVRQTFDNYESN----CFEVLLYKKNRTPVWFYMQIAPI 114
Cdd:pfam08447   1 IIYWSPRFEEILGYTPEELLGKGESWlDLVHPD--D---RERVREALWEALKGgepySGEYRIRRKDGEYRWVEARARPI 75

                          90
                  ....*....|...
gi 22024390   115 RNEHEKVVLFLCT 127
Cdd:pfam08447  76 RDENGKPVRVIGV 88
cyc_nuc_ocin TIGR03896
bacteriocin-type transport-associated protein; Members of this protein family are ...
 574-673 2.03e-03

bacteriocin-type transport-associated protein; Members of this protein family are uncharacterized and contain two copies of the cyclic nucleotide-binding domain pfam00027. Members are restricted to select cyanobacteria but are found regularly in association with a transport operon that, in turn, is associated with the production of putative bacteriocins. The models describing the transport operon are TIGR03794, TIGR03796, and TIGR03797.


Pssm-ID: 274839 [Multi-domain]  Cd Length: 317  Bit Score: 41.42  E-value: 2.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390   574 GDLIYHAGESVDALCFVVSGSLEV-IQDDE---VVAILGKGDVFGDIFWKETTLAhACANVRALTYCDLHIIKREALLKV 649
Cdd:TIGR03896 169 GTILIHEGGTVDALYILLYGEASLsISPDGpgrEVGSSRRGEILGETPFLNGSLP-GTATVKAIENSVLLAIDKQQLAAK 247

                          90       100
                  ....*....|....*....|....
gi 22024390   650 LDFYTAFANSFSRNLTLTCNLRKR 673
Cdd:TIGR03896 248 LQQDVGFASRFYRVIASLLSQRSR 271
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 14-132 3.31e-03

PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. [Regulatory functions, Small molecule interactions]


Pssm-ID: 272971 [Multi-domain]  Cd Length: 124  Bit Score: 38.43  E-value: 3.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390    14 TFLENIVRRSSESSFLLG-NAQIVDWpvvysNDGFCKLSGYHRADVMQKSSTcSFMYGELTDK--KTIEKVRQTFDNYES 90
Cdd:TIGR00229   3 ERYRAIFESSPDAIIVIDlEGNILYV-----NPAFEEIFGYSAEELIGRNVL-ELIPEEDREEvrERIERRLEGEPEPVS 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 22024390    91 NCFEVllYKKNRTPVWFYMQIAPIRnEHEKVVLFLCTFKDIT 132
Cdd:TIGR00229  77 EERRV--RRKDGSEIWVEVSVSPIR-TNGGELGVVGIVRDIT 115
PAS COG2202
PAS domain [Signal transduction mechanisms];
40-136 4.02e-03

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 40.39  E-value: 4.02e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22024390  40 VVYSNDGFCKLSGYHRADVMQKSSTcsfmygELTDKKTIEKVRQTFDN-----YESNCFEVLLYKKNRTPVWFYMQIAPI 114
Cdd:COG2202 159 ILYVNPAAEELLGYSPEELLGKSLL------DLLHPEDRERLLELLRRlleggRESYELELRLKDGDGRWVWVEASAVPL 232

                        90       100
                ....*....|....*....|..
gi 22024390 115 RNEHEkVVLFLCTFKDITLFKQ 136
Cdd:COG2202 233 RDGGE-VIGVLGIVRDITERKR 253
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 572-630 6.80e-03

Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel).


Pssm-ID: 462300 [Multi-domain]  Cd Length: 71  Bit Score: 36.08  E-value: 6.80e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 22024390   572 APGDLI---YHAGEsvDALCFVVSGSLEVIQDDEVVaILGKGDVFgdIFwkETTLAHACANV 630
Cdd:pfam07883   6 PPGESSpphRHPGE--DEFFYVLEGEGELTVDGEEV-VLKAGDSV--YF--PAGVPHRFRNT 60
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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